X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvamsas%2FSequencefeature.java;h=3d598d29768487faa7b490eff673b908cb60314c;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=360e7040ca95998709b13f1c8c1cab546c63374f;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git
diff --git a/src/jalview/io/vamsas/Sequencefeature.java b/src/jalview/io/vamsas/Sequencefeature.java
index 360e704..3d598d2 100644
--- a/src/jalview/io/vamsas/Sequencefeature.java
+++ b/src/jalview/io/vamsas/Sequencefeature.java
@@ -1,360 +1,360 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- *
- * This file is part of Jalview.
- *
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- * PURPOSE. See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
- */
-package jalview.io.vamsas;
-
-import java.util.Enumeration;
-import java.util.Vector;
-
-import uk.ac.vamsas.objects.core.DataSet;
-import uk.ac.vamsas.objects.core.DataSetAnnotations;
-import uk.ac.vamsas.objects.core.Link;
-import uk.ac.vamsas.objects.core.Property;
-import uk.ac.vamsas.objects.core.Provenance;
-import uk.ac.vamsas.objects.core.RangeAnnotation;
-import uk.ac.vamsas.objects.core.Score;
-import uk.ac.vamsas.objects.core.Seg;
-import uk.ac.vamsas.objects.core.Sequence;
-import uk.ac.vamsas.objects.utils.Properties;
-import jalview.bin.Cache;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.io.VamsasAppDatastore;
-import jalview.util.UrlLink;
-
-/**
- * @author JimP
- *
- */
-public class Sequencefeature extends Rangetype
-{
-
- uk.ac.vamsas.objects.core.DataSet dataset;
-
- uk.ac.vamsas.objects.core.Sequence sequence;
-
- private SequenceI dsSeq;
-
- public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,
- SequenceFeature sequenceFeature,
- uk.ac.vamsas.objects.core.DataSet dataset,
- uk.ac.vamsas.objects.core.Sequence sequence)
- {
- super(vamsasAppDatastore, sequenceFeature, DataSetAnnotations.class);
- this.dataset = dataset;
- this.sequence = sequence;
- doSync();
- }
-
- public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,
- DataSetAnnotations dseta, SequenceI dsSeq)
- {
- super(vamsasAppDatastore, dseta,
- jalview.datamodel.SequenceFeature.class);
- this.dsSeq = dsSeq;
- doJvUpdate();
- }
-
- public void addToDocument()
- {
- DataSetAnnotations dsa = (DataSetAnnotations) vobj;
- jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
- dsa = (DataSetAnnotations) getDSAnnotationFromJalview(
- new DataSetAnnotations(), feature);
- if (dsa.getProvenance() == null)
- {
- dsa.setProvenance(new Provenance());
- }
- addProvenance(dsa.getProvenance(), "created"); // JBPNote - need
- // to update
- dsa.addSeqRef(sequence); // we have just created this annotation
- // - so safe to use this
- bindjvvobj(feature, dsa);
- dataset.addDataSetAnnotations(dsa);
- }
-
- public void addFromDocument()
- {
- DataSetAnnotations dsa = (DataSetAnnotations) vobj;
- if (dsa.getSeqRefCount() != 1)
- {
- Cache.log
- .warn("Not binding "
- + dsa.getVorbaId()
- + " to Sequence Feature - has multiple dataset sequence references.");
- return;
- }
- jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;
- dsSeq.addSequenceFeature(sf = getJalviewSeqFeature(dsa));
- jvobj = sf;
- bindjvvobj(sf, dsa);
- }
-
- public void conflict()
- {
- log.warn("Untested sequencefeature conflict code");
- DataSetAnnotations dsa = (DataSetAnnotations) vobj;
- jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
- jalview.datamodel.SequenceFeature sf = getJalviewSeqFeature(dsa);
- replaceJvObjMapping(feature, sf); // switch binding of dsa from old feature
- // to newly created feature
- dsSeq.addSequenceFeature(sf); // add new imported feature
- addToDocument(); // and create a new feature in the document
- }
-
- public void updateToDoc()
- {
- DataSetAnnotations dsa = (DataSetAnnotations) vobj;
- jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
- if (dsa.getSeqRefCount() != 1)
- {
- replaceJvObjMapping(feature, null);
- Cache.log
- .warn("Binding of annotation to jalview feature has changed. Removing binding and recreating.");
- doSync(); // re-verify bindings.
- }
- else
- {
- // Sync the features from Jalview
- long oldref = dsa.get__last_hash();
- getDSAnnotationFromJalview(dsa, feature);
- if (oldref != dsa.hashCode())
- {
- Cache.log
- .debug("Updated dataset sequence annotation from feature.");
- addProvenance(dsa.getProvenance(), "modified");
- }
- }
-
- }
-
- public void updateFromDoc()
- {
- DataSetAnnotations dsa = (DataSetAnnotations) vobj;
- jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
- if (dsa.getSeqRefCount() != 1)
- {
- // conflicting update from document - we cannot map this feature anymore.
- replaceJvObjMapping(feature, null);
- Cache.log
- .warn("annotation ("
- + dsa.getVorbaId()
- + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
- // - consider deleting the feature ?
- dsSeq.deleteFeature(feature);
- // doSync();
- }
- else
- {
- // Sync the features to Jalview - easiest to delete and add the feature
- // again
- jalview.datamodel.SequenceFeature newsf = getJalviewSeqFeature(dsa);
- dsSeq.deleteFeature(feature);
- replaceJvObjMapping(feature, newsf);
- dsSeq.addSequenceFeature(newsf);
- if (feature.otherDetails != null)
- {
- // TODO later: leave this to finalise method ?
- feature.otherDetails.clear();
- }
- }
- }
-
- /**
- * correctly create/update a RangeAnnotation from a jalview sequence feature
- * TODO: refactor to a method in jalview.io.vamsas.RangeAnnotation class
- *
- * @param dsa
- * (typically DataSetAnnotations or AlignmentSequenceAnnotation)
- * @param feature
- * (the feature to be mapped from)
- * @return
- */
- private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,
- jalview.datamodel.SequenceFeature feature)
- {
- dsa.setType(feature.getType());
- Seg vSeg = new Seg();
- vSeg.setStart(feature.getBegin());
- vSeg.setEnd(feature.getEnd());
- vSeg.setInclusive(true);
- if (dsa.getSegCount() > 1)
- {
- Cache.log
- .debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
- + dsa.getVorbaId() + ")");
- }
- dsa.setSeg(new Seg[]
- { vSeg });
- dsa.setDescription(feature.getDescription());
- dsa.setStatus(feature.getStatus());
- if (feature.links != null && feature.links.size() > 0)
- {
- for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
- {
- String link = (String) feature.links.elementAt(i);
- UrlLink ulink = new UrlLink(link);
- if (ulink.isValid())
- {
- // We only add static links to the document.
- Link vLink = new Link();
- vLink.setContent(ulink.getLabel());
- vLink.setHref(ulink.getTarget());
- dsa.addLink(vLink);
- }
- }
- }
- dsa.setGroup(feature.getFeatureGroup());
- if (feature.getScore() != Float.NaN)
- {
- Score fscore = new Score();
- dsa.setScore(new Score[]
- { fscore });
- fscore.setContent(feature.getScore());
- fscore.setName(feature.getType());
- }
- if (feature.otherDetails != null)
- {
- Enumeration iter = feature.otherDetails.keys();
- Vector props = dsa.getPropertyAsReference();
- while (iter.hasMoreElements())
- {
- String key = (String) iter.nextElement();
- if (!key.equalsIgnoreCase("score")
- && !key.equalsIgnoreCase("status"))
- {
- Property nprop = new Property();
- nprop.setName(key);
- Object vlu = feature.getValue(key);
- nprop.setContent(feature.getValue(key).toString());
- boolean valid = false;
- if (vlu instanceof String)
- {
- nprop.setType(uk.ac.vamsas.objects.utils.Properties.STRINGTYPE);
- valid = true;
- }
- else if (vlu instanceof Integer)
- {
- valid = true;
- nprop
- .setType(uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
- }
- else if (vlu instanceof Float)
- {
- nprop.setType(uk.ac.vamsas.objects.utils.Properties.FLOATTYPE);
- valid = true;
- }
- if (valid)
- {
- if (props != null)
- {
- uk.ac.vamsas.objects.utils.Properties.addOrReplace(props,
- nprop);
- }
- else
- {
- dsa.addProperty(nprop);
- }
- }
- }
- }
- }
- return dsa;
- }
-
- private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)
- {
- int[] se = getBounds(dseta);
- SequenceFeature sf = new jalview.datamodel.SequenceFeature(dseta
- .getType(), dseta.getDescription(), dseta.getStatus(), se[0],
- se[1], dseta.getGroup());
- if (dseta.getLinkCount() > 0)
- {
- Link[] links = dseta.getLink();
- for (int i = 0; i < links.length; i++)
- {
- // TODO: use URLLink parsing/validation here.
- sf.addLink(links[i].getContent() + "|" + links[i].getHref());
- }
- }
- if (dseta.getScoreCount() > 0)
- {
- Enumeration scr = dseta.enumerateScore();
- while (scr.hasMoreElements())
- {
- Score score = (Score) scr.nextElement();
- if (score.getName().equals(sf.getType()))
- {
- sf.setScore(score.getContent());
- }
- else
- {
- sf.setValue(score.getName(), "" + score.getContent());
- }
- }
- }
- // other details
- Enumeration props = dseta.enumerateProperty();
- while (props.hasMoreElements())
- {
- Property p = (Property) props.nextElement();
- Object val = null;
- if (Properties.isValid(p))
- {
- if (Properties.isString(p))
- {
- val = p.getContent();
- }
- if (Properties.isBoolean(p))
- {
- try
- {
- val = new Boolean(p.getContent());
- } catch (Exception e)
- {
- }
- }
- if (Properties.isFloat(p))
- {
- try
- {
- val = new Float(p.getContent());
-
- } catch (Exception e)
- {
- }
- }
- if (Properties.isInteger(p))
- {
- try
- {
- val = new Integer(p.getContent());
- } catch (Exception e)
- {
- }
- }
- if (val != null)
- {
- sf.setValue(p.getName(), val);
- }
- }
- }
-
- return sf;
- }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io.vamsas;
+
+import java.util.Enumeration;
+import java.util.Vector;
+
+import uk.ac.vamsas.objects.core.DataSetAnnotations;
+import uk.ac.vamsas.objects.core.Link;
+import uk.ac.vamsas.objects.core.Property;
+import uk.ac.vamsas.objects.core.Provenance;
+import uk.ac.vamsas.objects.core.RangeAnnotation;
+import uk.ac.vamsas.objects.core.Score;
+import uk.ac.vamsas.objects.core.Seg;
+import uk.ac.vamsas.objects.utils.Properties;
+import jalview.bin.Cache;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.VamsasAppDatastore;
+import jalview.util.UrlLink;
+
+/**
+ * @author JimP
+ *
+ */
+public class Sequencefeature extends Rangetype
+{
+
+ uk.ac.vamsas.objects.core.DataSet dataset;
+
+ uk.ac.vamsas.objects.core.Sequence sequence;
+
+ private SequenceI dsSeq;
+
+ public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,
+ SequenceFeature sequenceFeature,
+ uk.ac.vamsas.objects.core.DataSet dataset,
+ uk.ac.vamsas.objects.core.Sequence sequence)
+ {
+ super(vamsasAppDatastore, sequenceFeature, DataSetAnnotations.class);
+ this.dataset = dataset;
+ this.sequence = sequence;
+ doSync();
+ }
+
+ public Sequencefeature(VamsasAppDatastore vamsasAppDatastore,
+ DataSetAnnotations dseta, SequenceI dsSeq)
+ {
+ super(vamsasAppDatastore, dseta,
+ jalview.datamodel.SequenceFeature.class);
+ this.dsSeq = dsSeq;
+ doJvUpdate();
+ }
+
+ public void addToDocument()
+ {
+ DataSetAnnotations dsa = (DataSetAnnotations) vobj;
+ jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
+ dsa = (DataSetAnnotations) getDSAnnotationFromJalview(
+ new DataSetAnnotations(), feature);
+ if (dsa.getProvenance() == null)
+ {
+ dsa.setProvenance(new Provenance());
+ }
+ addProvenance(dsa.getProvenance(), "created"); // JBPNote - need
+ // to update
+ dsa.addSeqRef(sequence); // we have just created this annotation
+ // - so safe to use this
+ bindjvvobj(feature, dsa);
+ dataset.addDataSetAnnotations(dsa);
+ }
+
+ public void addFromDocument()
+ {
+ DataSetAnnotations dsa = (DataSetAnnotations) vobj;
+ if (dsa.getSeqRefCount() != 1)
+ {
+ Cache.log
+ .warn("Not binding "
+ + dsa.getVorbaId()
+ + " to Sequence Feature - has multiple dataset sequence references.");
+ return;
+ }
+ jalview.datamodel.SequenceFeature sf = (jalview.datamodel.SequenceFeature) jvobj;
+ dsSeq.addSequenceFeature(sf = getJalviewSeqFeature(dsa));
+ jvobj = sf;
+ bindjvvobj(sf, dsa);
+ }
+
+ public void conflict()
+ {
+ log.warn("Untested sequencefeature conflict code");
+ DataSetAnnotations dsa = (DataSetAnnotations) vobj;
+ jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
+ jalview.datamodel.SequenceFeature sf = getJalviewSeqFeature(dsa);
+ replaceJvObjMapping(feature, sf); // switch binding of dsa from old feature
+ // to newly created feature
+ dsSeq.addSequenceFeature(sf); // add new imported feature
+ addToDocument(); // and create a new feature in the document
+ }
+
+ public void updateToDoc()
+ {
+ DataSetAnnotations dsa = (DataSetAnnotations) vobj;
+ jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
+ if (dsa.getSeqRefCount() != 1)
+ {
+ replaceJvObjMapping(feature, null);
+ Cache.log
+ .warn("Binding of annotation to jalview feature has changed. Removing binding and recreating.");
+ doSync(); // re-verify bindings.
+ }
+ else
+ {
+ // Sync the features from Jalview
+ long oldref = dsa.get__last_hash();
+ getDSAnnotationFromJalview(dsa, feature);
+ if (oldref != dsa.hashCode())
+ {
+ Cache.log
+ .debug("Updated dataset sequence annotation from feature.");
+ addProvenance(dsa.getProvenance(), "modified");
+ }
+ }
+
+ }
+
+ public void updateFromDoc()
+ {
+ DataSetAnnotations dsa = (DataSetAnnotations) vobj;
+ jalview.datamodel.SequenceFeature feature = (jalview.datamodel.SequenceFeature) jvobj;
+ if (dsa.getSeqRefCount() != 1)
+ {
+ // conflicting update from document - we cannot map this feature anymore.
+ replaceJvObjMapping(feature, null);
+ Cache.log
+ .warn("annotation ("
+ + dsa.getVorbaId()
+ + " bound to jalview feature cannot be mapped. Removing binding, deleting feature, and deleting feature.");
+ // - consider deleting the feature ?
+ dsSeq.deleteFeature(feature);
+ // doSync();
+ }
+ else
+ {
+ // Sync the features to Jalview - easiest to delete and add the feature
+ // again
+ jalview.datamodel.SequenceFeature newsf = getJalviewSeqFeature(dsa);
+ dsSeq.deleteFeature(feature);
+ replaceJvObjMapping(feature, newsf);
+ dsSeq.addSequenceFeature(newsf);
+ if (feature.otherDetails != null)
+ {
+ // TODO later: leave this to finalise method ?
+ feature.otherDetails.clear();
+ }
+ }
+ }
+
+ /**
+ * correctly create/update a RangeAnnotation from a jalview sequence feature
+ * TODO: refactor to a method in jalview.io.vamsas.RangeAnnotation class
+ *
+ * @param dsa
+ * (typically DataSetAnnotations or AlignmentSequenceAnnotation)
+ * @param feature
+ * (the feature to be mapped from)
+ * @return
+ */
+ private RangeAnnotation getDSAnnotationFromJalview(RangeAnnotation dsa,
+ jalview.datamodel.SequenceFeature feature)
+ {
+ dsa.setType(feature.getType());
+ Seg vSeg = new Seg();
+ vSeg.setStart(feature.getBegin());
+ vSeg.setEnd(feature.getEnd());
+ vSeg.setInclusive(true);
+ if (dsa.getSegCount() > 1)
+ {
+ Cache.log
+ .debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
+ + dsa.getVorbaId() + ")");
+ }
+ dsa.setSeg(new Seg[]
+ { vSeg });
+ dsa.setDescription(feature.getDescription());
+ dsa.setStatus(feature.getStatus());
+ if (feature.links != null && feature.links.size() > 0)
+ {
+ for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
+ {
+ String link = (String) feature.links.elementAt(i);
+ UrlLink ulink = new UrlLink(link);
+ if (ulink.isValid())
+ {
+ // We only add static links to the document.
+ Link vLink = new Link();
+ vLink.setContent(ulink.getLabel());
+ vLink.setHref(ulink.getTarget());
+ dsa.addLink(vLink);
+ }
+ }
+ }
+ dsa.setGroup(feature.getFeatureGroup());
+ if (feature.getScore() != Float.NaN)
+ {
+ Score fscore = new Score();
+ dsa.setScore(new Score[]
+ { fscore });
+ fscore.setContent(feature.getScore());
+ fscore.setName(feature.getType());
+ }
+ if (feature.otherDetails != null)
+ {
+ Enumeration iter = feature.otherDetails.keys();
+ Vector props = dsa.getPropertyAsReference();
+ while (iter.hasMoreElements())
+ {
+ String key = (String) iter.nextElement();
+ if (!key.equalsIgnoreCase("score")
+ && !key.equalsIgnoreCase("status"))
+ {
+ Property nprop = new Property();
+ nprop.setName(key);
+ Object vlu = feature.getValue(key);
+ nprop.setContent(feature.getValue(key).toString());
+ boolean valid = false;
+ if (vlu instanceof String)
+ {
+ nprop.setType(uk.ac.vamsas.objects.utils.Properties.STRINGTYPE);
+ valid = true;
+ }
+ else if (vlu instanceof Integer)
+ {
+ valid = true;
+ nprop.setType(uk.ac.vamsas.objects.utils.Properties.INTEGERTYPE);
+ }
+ else if (vlu instanceof Float)
+ {
+ nprop.setType(uk.ac.vamsas.objects.utils.Properties.FLOATTYPE);
+ valid = true;
+ }
+ if (valid)
+ {
+ if (props != null)
+ {
+ uk.ac.vamsas.objects.utils.Properties.addOrReplace(props,
+ nprop);
+ }
+ else
+ {
+ dsa.addProperty(nprop);
+ }
+ }
+ }
+ }
+ }
+ return dsa;
+ }
+
+ private SequenceFeature getJalviewSeqFeature(RangeAnnotation dseta)
+ {
+ int[] se = getBounds(dseta);
+ SequenceFeature sf = new jalview.datamodel.SequenceFeature(
+ dseta.getType(), dseta.getDescription(), dseta.getStatus(),
+ se[0], se[1], dseta.getGroup());
+ if (dseta.getLinkCount() > 0)
+ {
+ Link[] links = dseta.getLink();
+ for (int i = 0; i < links.length; i++)
+ {
+ // TODO: use URLLink parsing/validation here.
+ sf.addLink(links[i].getContent() + "|" + links[i].getHref());
+ }
+ }
+ if (dseta.getScoreCount() > 0)
+ {
+ Enumeration scr = dseta.enumerateScore();
+ while (scr.hasMoreElements())
+ {
+ Score score = (Score) scr.nextElement();
+ if (score.getName().equals(sf.getType()))
+ {
+ sf.setScore(score.getContent());
+ }
+ else
+ {
+ sf.setValue(score.getName(), "" + score.getContent());
+ }
+ }
+ }
+ // other details
+ Enumeration props = dseta.enumerateProperty();
+ while (props.hasMoreElements())
+ {
+ Property p = (Property) props.nextElement();
+ Object val = null;
+ if (Properties.isValid(p))
+ {
+ if (Properties.isString(p))
+ {
+ val = p.getContent();
+ }
+ if (Properties.isBoolean(p))
+ {
+ try
+ {
+ val = new Boolean(p.getContent());
+ } catch (Exception e)
+ {
+ }
+ }
+ if (Properties.isFloat(p))
+ {
+ try
+ {
+ val = new Float(p.getContent());
+
+ } catch (Exception e)
+ {
+ }
+ }
+ if (Properties.isInteger(p))
+ {
+ try
+ {
+ val = new Integer(p.getContent());
+ } catch (Exception e)
+ {
+ }
+ }
+ if (val != null)
+ {
+ sf.setValue(p.getName(), val);
+ }
+ }
+ }
+
+ return sf;
+ }
+
+}